Can I restrict certain atoms in a ligand from binding to a protein when performing molecular docking? If so, what tools can help me to do this?

Lucindah Fry- Nartey @Lucindah-Fry-Nartey

10 January 2023 1 9K Report

I would prefer certain atoms in a particular ligand to not be involved in the molecular docking process because I know that they bind to other proteins in a biological situation. I want to restrict them to be able to mimic the natural biological system as closely as possible.

Annemarie Honegger

You might look at this paper on docking with constraints:

Article MedusaDock 2.0: Efficient and Accurate Protein-Ligand Dockin...

Look at the documentation for the docking program you are using to find out whether it does support constraints and how to set these.

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